3-48190429-T-G

Variant names:

• chr3-48190429-T-G
• rs1903061

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.931 in 152,018 control chromosomes in the GnomAD database, including 66,004 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.93 (66004 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.931 AC: 141356 AN: 151900 Hom.: 65947 Cov.: 29

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.951

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.973

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.932

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.931 AC: 141472 AN: 152018 Hom.: 66004 Cov.: 29 AF XY: 0.930 AC XY: 69093 AN XY: 74264

African (AFR) AF: 0.984 AC: 40780 AN: 41464

American (AMR) AF: 0.951 AC: 14532 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3307 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5139 AN: 5142

South Asian (SAS) AF: 0.972 AC: 4672 AN: 4806

European-Finnish (FIN) AF: 0.866 AC: 9157 AN: 10578

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60841 AN: 67980

Other (OTH) AF: 0.933 AC: 1961 AN: 2102

Alfa AF: 0.919 Hom.: 14891

Bravo AF: 0.941

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.1
DANN	Benign	0.74
PhyloP100		-0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1903061; hg19: chr3-48231919;